Metadata-Version: 2.1
Name: dbispipeline
Version: 0.5.0
Summary: should make things more reproducible
Home-page: https://git.uibk.ac.at/dbis/software/dbispipeline
Author: Benjamin Murauer, Michael Vötter
Author-email: b.murauer@posteo.de
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: gitpython (>2)
Requires-Dist: matplotlib
Requires-Dist: pandas
Requires-Dist: psycopg2-binary
Requires-Dist: scikit-learn
Requires-Dist: sqlalchemy (>1.3)
Requires-Dist: click

# DBIS Pipeline
This pipline can be used to run analyses in a structured way.

## Usage

the user writes a minimal configuration file which contains only the following
information:
 * "how do I get the data?", by providing a dataloader
 * "what to do with the data?", by providing a scikit pipeline
 * "what to do with the result?", by providing output handlers.

Please have a look at the examples for more information.

## Requirements

`pipenv`

everything else should be installed by pipenv.

## Installation

1. Create a fresh directory.
2. In that directory, call `pipenv install dbispipeline`
   This call will install a virtual environment as well as all dependencies.
3. Write your configuration(s)
4. call `pipenv run python -m dbispipeline <yourconfigurationfile.py>`

Enjoy!


## Configuration
The framework look in multiple directories for its configuration files.
* `/usr/local/etc/dbispipeline.ini` used for system wide default.
* `$HOME/.config/dbispipeline.ini` used for user specific configurations.
* `./dbispipeline.ini` for project sepcifig configurations.

And example configuration file looks like this:
```ini
[database]

# url to your postgres database
host = your.personal.database

# your database user name
user = user

# port of your postgres database, default = 5432
# port = 5432

# password of your database user
password = <secure-password>

# database to use
database = pipelineresults

# table to be used
result_table = my_super_awesome_results

[project]
# this will be stored in the database
name = dbispipeline-test

[mail]
# email address to use as sender
sender = botname@yourserver.com

# recipient. This should probably be set on a home-directory-basis.
recipient = you@yourserver.com

# smtp server address to use
smtp_server = smtp.yourserver.com

# use smtp authentication, default = no
# authenticate = no

# username for smtp authentication, required if authenticate = yes
# username = foo

# password for smtp authentication, required if authenticate = yes
# password = bar

# port to use for smtp server connection, default = 465
# port = 465
```




